Chemistry of LifeChemistry of Life

Chapter 2Chapter 2

How are living things (biotic) and non-How are living things (biotic) and non-living (abiotic) things different?living (abiotic) things different?

How are they the same?How are they the same?

All composed of AtomsAll composed of Atoms

Element = Element = substance that can’t be broken substance that can’t be broken down into simpler chemical down into simpler chemical substances.substances.

1.1. Represented by 1 or 2 letter codeRepresented by 1 or 2 letter code

(H, O, Na, Cl, He, Ne…)(H, O, Na, Cl, He, Ne…)

2.2. Made up of Made up of atomsatoms

Atoms = Atoms = smallest particle of an element smallest particle of an element that has characteristics of that elementthat has characteristics of that element..

Structure of an AtomStructure of an AtomIn the NucleusIn the Nucleus:: mass of the atom mass of the atom

Protons (pProtons (p++)) – positive charge – positive charge

Neutrons (nNeutrons (n00)) – no charge (neutral) – no charge (neutral)In the Electron CloudIn the Electron Cloud: space of atom: space of atom

Electrons (e-)Electrons (e-) – negative charge; in – negative charge; in constant motion revolving around nucleusconstant motion revolving around nucleus

7 different energy levels; each can only 7 different energy levels; each can only hold a set amount of electronshold a set amount of electrons

IONSIONSAtoms or group of atoms with a Atoms or group of atoms with a

positive or negative chargepositive or negative chargeFormed by loss or gain of electronsFormed by loss or gain of electrons

Combination of SubstancesCombination of SubstancesMixtureMixture::

Physical combinationPhysical combination of 2 or more things. of 2 or more things.

Each substance Each substance keeps its original properties.keeps its original properties.

Compound:Compound:

Chemical combinationChemical combination of 2 or more of 2 or more elements.elements.

The substances The substances lose their original properties lose their original properties and form something newand form something new..

BondingBonding

Combination of elements with Combination of elements with electrons to become more stableelectrons to become more stable

Atoms want to have full outer eAtoms want to have full outer e-- level level

2 e2 e-- in 1 in 1stst level level

8 e8 e-- in 2 in 2ndnd through 7 through 7thth levels levels

Covalent BondingCovalent Bonding::

SharingSharing of electrons between atoms of electrons between atoms

example: Water (Hexample: Water (H22O)O)

Ionic BondingIonic Bonding::

TransferringTransferring of electrons between atoms of electrons between atoms

Example: Table Salt (NaCl)Example: Table Salt (NaCl)

Chemical ReactionsChemical Reactionsforming or breaking of bondsforming or breaking of bonds between between

atomsatomscauses causes substances to combine and substances to combine and

recombinerecombine to form molecules or to form molecules or compounds. compounds.

Occur only when conditions are rightOccur only when conditions are right

MetabolismMetabolism = chemical reactions that = chemical reactions that occur over and over inside our cellsoccur over and over inside our cells

Measuring Acids and BasesMeasuring Acids and Baseschemical reactions depend on how acidic or chemical reactions depend on how acidic or

basic the environment isbasic the environment is Indicators = pH paper, litmus, and other Indicators = pH paper, litmus, and other

substances that change colorsubstances that change colorpH = a measure of how acidic or basic a pH = a measure of how acidic or basic a

solution is.solution is. Scale from 0 to 14Scale from 0 to 14

0 = strongest acid (lots of Hydrogen ions)0 = strongest acid (lots of Hydrogen ions)7 = neutral7 = neutral14 = strongest base (few hydrogen ions)14 = strongest base (few hydrogen ions)

Acids:Acids:Sour taste (fruits)Sour taste (fruits)forms forms hydrogen ions (H+)hydrogen ions (H+) in water in waterabundance of abundance of H+ ionsH+ ionspH below 7pH below 7, the lower the pH the , the lower the pH the

stronger the acid (Strong Acid = pH stronger the acid (Strong Acid = pH 1; Weak Acid = pH 6.9)1; Weak Acid = pH 6.9)

ex: HCl, Hex: HCl, H22SOSO44, HC, HC22HH33OO22 … …

ACIDSACIDS and and BASESBASES

Bases:Bases:Bitter taste, slippery, good cleanersBitter taste, slippery, good cleanersforms forms hydroxide ions hydroxide ions (OH-) in water(OH-) in waterabundance of abundance of OH- ionsOH- ionsHas a Has a pH above 7pH above 7, higher the pH , higher the pH

the stronger the base (Strong base the stronger the base (Strong base = pH 14; Weak base = pH 7.1)= pH 14; Weak base = pH 7.1)

Ex: NaOH, NHEx: NaOH, NH33 … …

Organic MoleculesOrganic MoleculesMolecules involved in lifeMolecules involved in lifeHONC 1234HONC 1234 = rule to describe most = rule to describe most

common organic elements and their common organic elements and their bonding patterns.bonding patterns.

H – hydrogen - 1 bondH – hydrogen - 1 bondO – oxygen – 2 bondsO – oxygen – 2 bondsN – Nitrogen – 3 bondsN – Nitrogen – 3 bondsC – carbon – 4 bondsC – carbon – 4 bonds

Role of Carbon Role of Carbon in Organismsin Organisms

Properties of Carbon:Properties of Carbon:

1.1. Natures tinker toyNatures tinker toy

2.2. 4 electrons in outer shell 4 electrons in outer shell

3.3. Forms Forms 4 covalent bonds4 covalent bonds to become to become stable (stable (single, double, or triple bondssingle, double, or triple bonds))

4.4. Forms chains, branched chains, and Forms chains, branched chains, and ringsrings

Image of carbon skeletonsImage of carbon skeletons

IsomersIsomersMolecules with Molecules with

same chemical same chemical formula, but formula, but different structural different structural arrangements.arrangements.

Each has different Each has different propertiesproperties

Ex: Glucose and Ex: Glucose and Fructose (CFructose (C66HH1212OO66))

Building BlocksBuilding Blocks50 common building blocks to carry out 50 common building blocks to carry out

life’s functionslife’s functionsMonomerMonomer – – small moleculesmall molecule building building

block of lifeblock of lifeEx: glucoseEx: glucosePolymerPolymer – molecule formed when – molecule formed when

monomers are linked togethermonomers are linked togetherEx: cellulose is a polymer of glucoseEx: cellulose is a polymer of glucose

Condensation Condensation andand

Hydrolysis Hydrolysis ReactionsReactions

Condensation ReactionCondensation Reaction

Chemical reaction that occurs when Chemical reaction that occurs when monomers are linked together to form monomers are linked together to form polymers.polymers.

Creates 1 water (HCreates 1 water (H22O) molecule per O) molecule per

linklinkAlso called synthesis or dehydrationAlso called synthesis or dehydration

Hydrolysis ReactionHydrolysis Reaction

Chemical reaction that occurs when Chemical reaction that occurs when polymers are broken down into polymers are broken down into monomersmonomers

Addition of 1 water (HAddition of 1 water (H22O) for each O) for each

broken linkbroken linkOccurs during digestion, decompositionOccurs during digestion, decomposition

Condensation Condensation andand

Hydrolysis Hydrolysis ReactionsReactions

Types of Organic MoleculesTypes of Organic Molecules

CarbohydratesCarbohydratesLipidsLipidsProteinsProteinsNucleic AcidsNucleic Acids

These 4 groups of These 4 groups of organic molecules, organic molecules, their monomers, their monomers, polymers, and polymers, and functions, are basic functions, are basic and essential to and essential to biology!biology!

CARBOHYDRATES CARBOHYDRATES (starches and sugars)(starches and sugars)

FunctionFunction – store energy for short – store energy for short term; sometimes used for structural term; sometimes used for structural supportsupport

StructureStructure

1.1. Composed of C, H, and OComposed of C, H, and O

2.2. Ratio of 2 H for every 1 ORatio of 2 H for every 1 O

3.3. Monosaccharide – single sugarMonosaccharide – single sugar

1.1. Glucose (blood sugar), fructose (fruit Glucose (blood sugar), fructose (fruit sugar)sugar)

4.4. Disaccharide – two sugarsDisaccharide – two sugars

1.1. Sucrose (table sugar – glucose + Sucrose (table sugar – glucose + fructose)fructose)

5.5. Polysaccharide – many sugarsPolysaccharide – many sugars

1.1. Starch – storage in plants Starch – storage in plants (potatoes)(potatoes)

2.2. Glycogen – storage in animal Glycogen – storage in animal muscle and liver cellsmuscle and liver cells

3.3. Cellulose – fiber in plants (wood, Cellulose – fiber in plants (wood, paper)paper)

LIPIDS LIPIDS (fats, oils, waxes, steroids)(fats, oils, waxes, steroids)

Functions:Functions:1.1. Long term energy storageLong term energy storage

2.2. Insulation, cushioning of organsInsulation, cushioning of organs

3.3. Waterproofing (waxes)Waterproofing (waxes)

4.4. Chemical messengers in body Chemical messengers in body (steroids)(steroids)

Properties:Properties:1.1. Composed of C, H, and OComposed of C, H, and O

2.2. Much Much less oxygenless oxygen than carbon or than carbon or hydrogenhydrogen

1.1. Beef fat = CBeef fat = C5757HH110110OO66

3.3. Nonpolar – no net electrical chargeNonpolar – no net electrical charge

1.1. Insoluble in waterInsoluble in water

Triglycerides Triglycerides = type of fat= type of fat

1.1. Composed of 3 fatty acids Composed of 3 fatty acids (monomers) and 1 glycerol (sugar)(monomers) and 1 glycerol (sugar)

2.2. Saturated fat = solid at room temp, Saturated fat = solid at room temp, lacks double bonds between lacks double bonds between carbons.carbons.

3.3. Unsaturated fat = liquid at room Unsaturated fat = liquid at room temp (oils), at least 1 double bond temp (oils), at least 1 double bond between carbon atoms somewhere between carbon atoms somewhere in fatty acid chainin fatty acid chain

TriglyceridTriglyceridee

SteroidsSteroids

1.1. 4 connected carbon ring structures4 connected carbon ring structures

2.2. Used as chemical messengers in bodyUsed as chemical messengers in body

Ex: sex hormones (testosterone and Ex: sex hormones (testosterone and estrogen)estrogen)

PhospholipidsPhospholipids

1.1. Composed of 2 fatty acids, glycerol, Composed of 2 fatty acids, glycerol, and a phosphate groupand a phosphate group

2.2. Major component of cell membraneMajor component of cell membrane

A SteroidA Steroid

PhospholipidPhospholipid

PROTIENSPROTIENS

Functions:Functions:

1.1. Structure – hair, finger nails, skinStructure – hair, finger nails, skin

2.2. AntibodiesAntibodies

3.3. HormonesHormones

4.4. Movement – musclesMovement – muscles

5.5. Enzymes – proteins that speed up Enzymes – proteins that speed up chemical reactions in the bodychemical reactions in the body

1.1. 10,000 types of enzymes, each has 10,000 types of enzymes, each has a different functiona different function

StructureStructure

1.1. Composed of C, H, O, N, and Composed of C, H, O, N, and sometimes Ssometimes S

2.2. Made of monomers called amino acids Made of monomers called amino acids (20 different types)(20 different types)

3.3. Amino acids consist of central carbon Amino acids consist of central carbon with the following attachedwith the following attached

1.1. HydrogenHydrogen

2.2. Amine group, NH2Amine group, NH2

3.3. Carboxyl group COOHCarboxyl group COOH

4.4. R-group – What makes the A.A. different R-group – What makes the A.A. different from the rest. (R can be one of 20 different from the rest. (R can be one of 20 different groups, from a simple H to a ringed groups, from a simple H to a ringed structure)structure)

4.4. Peptide BondPeptide Bond = covalent bond formed = covalent bond formed when when amino acids link togetheramino acids link together to form to form proteins.proteins.

Polypeptide formationPolypeptide formation

NUCLEIC ACIDSNUCLEIC ACIDS(DNA and RNA)(DNA and RNA)

StructureStructure

1.1. Composed of C, H, O, N, and PComposed of C, H, O, N, and P

2.2. Monomers = nucleotidesMonomers = nucleotides

1.1. Sugar – ribose or deoxyriboseSugar – ribose or deoxyribose

2.2. Phosphate groupPhosphate group

3.3. Nitrogen Base – A, T, G, C, and UNitrogen Base – A, T, G, C, and U

Function:Function:

1.1. Information StorageInformation Storage

2.2. Heredity – DNA is used to pass genetic Heredity – DNA is used to pass genetic info to next generationinfo to next generation

3.3. Direct cell activities – RNA directs Direct cell activities – RNA directs synthesis of proteinssynthesis of proteins

NucleotideNucleotide

Double helixDouble helix

Revisiting Enzymes:Revisiting Enzymes:28 days to digest food without enzymes, 28 days to digest food without enzymes,

only 2-4 hours with enzymes!only 2-4 hours with enzymes!CatalystCatalyst - substance that - substance that speeds up speeds up

chemical reactionschemical reactions w/o being consumed w/o being consumed by the reaction (recycled)by the reaction (recycled)

substratesubstrate - molecule(s) - molecule(s) going through going through chemical reactionchemical reaction

productproduct - -new molecule(s) formednew molecule(s) formed after after chemical reactionchemical reaction

active siteactive site - - placeplace on enzyme on enzyme where where substrate fitssubstrate fits, like a hand in a glove., like a hand in a glove.

substrate specificsubstrate specific - each enzyme will - each enzyme will only react with the substrate that fits the only react with the substrate that fits the active siteactive site

denaturationdenaturation - a - a change in the active change in the active sitesite so it so it no longer reacts with the no longer reacts with the substratesubstrate, may be , may be caused by extremes caused by extremes in temperature, pH, or toxinsin temperature, pH, or toxins

Protein denaturation